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Sample GSM510538 Query DataSets for GSM510538
Status Public on Feb 17, 2010
Title AG09319-DS12286
Sample type RNA
Source name Adult human gum tissue fibroblasts
Organism Homo sapiens
Characteristics cell type: Adult human gum tissue fibroblasts
Biomaterial provider Coriell;AG09319
Growth protocol Followed vendor recommendations for growth protocol/media
Extracted molecule total RNA
Extraction protocol At cell harvest, a subset of cells was stored at -20oC in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).
Label biotin
Label protocol A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.
Hybridization protocol Hybridizations were carried out according the manufacturer (Affymetrix) protocol
Scan protocol Affymterix Gene Chip Scanner 3000
Description Adult human gum tissue fibroblasts
Data processing Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
Probe group file used for analysis: HuEx-1_0-st-v2.r2.pgf
Submission date Feb 17, 2010
Last update date Apr 23, 2013
Contact name ENCODE DCC
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
Platform ID GPL5188
Series (1)
GSE19090 Exon arrays of ENCODE tier 1, tier 2 and tier 3 cell types

Data table header descriptions
VALUE quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

Data table
2315101 113.2144
2315102 139.9674
2315104 101.3662
2315105 30.22557
2315107 79.95387
2315114 53.5335
2315126 50.43369
2315132 20.87309
2315133 72.41151
2315134 1.76286
2315138 81.82722
2315140 44.3174
2315142 8.702643
2315144 9.354708
2315146 34.85732
2315148 187.2817
2315149 193.7155
2315150 85.22248
2315151 3.507959
2315153 63.45348

Total number of rows: 1384231

Table truncated, full table size 22725 Kbytes.

Supplementary file Size Download File type/resource
GSM510538_X_Hs_AG09319_E_091208_03_DS12286_W.CEL.gz 23.7 Mb (ftp)(http) CEL
GSM510538_wgEncodeUwAffyExonArrayAg09319SimpleSignalRep2.broadPeak.gz 21.0 Mb (ftp)(http) BROADPEAK
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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